Part 2: Setup of Data Server (Public Sharing)

Transcription

1 Version 2.1, September 3, 2012

2 Contents 1. Introduction Getting Access Authorizations and Registration of Host Information to DNS Requirements for Data Server Flow Chart of Setup of Data Server and Manual Chapters Setup of Linux OS Installation of CentOS Download Installation Setup Window Initialization of CentOS Confirmation of Needed Packages Installation of Java Configuration of Local Security Confirmation of Settings Setup of MassBank System Installation of the Linux version of MassBank Download Expanding Archive File Configuration of Tomcat Environment Configuration of Installation Environment Installation Initialization of MassBank Editing of the MassBank Configuration File Editing of hosts file Change of Preset User ID and Password of Administration Tool Reboot of Data Server Check of Data Server Check of MassBank System Registration to MassBank Group Request of Data Server Registration Request of Prefix of MassBank Record ID Part 2-2

3 1. Introduction Purpose MassBank is a distributed database. Research groups have to provide their own data servers, from which they contribute their mass spectral data. Part 2: Setup of Data Server (Public Sharing) of Data Publication Manual shows the procedure of the setup of data server; Linux OS, MassBank System for Linux, and other necessary software are installed and configured on the data server. - Part 2 assumes that administrators have a certain degree of knowledge on Linux OS. 1.1 Getting Access Authorizations and Registration of Host Information to DNS From the network administrator of your department or institute, get authorizations to set up the data server and to allow the following accesses. These authorizations are essential for the access to the server. Access Authorizations HTTP access authorization (free port number TCP/80) SSH access authorization (free port number TCP/22) (*1) *1) The update of the MassBank system is made simultaneously on all the MassBank data servers because MassBank is a distributed database. MassBank project would make the SSH access to the data servers for the update. The SSH access could be restricted only from a specific IP address ( ) of the MassBank project in a peer-to-peer fashion. This requires the authorization of SSH and HTTP accesses from your network administrator. Get the server host name in the URL to publish data (see Edit the MassBank Configuration File ). Server host name is required for the setup. Server host name that is set in DNS Server Host Name Part 2-3

4 1.2 Requirements for Data Server Hardware requirements are recommended requirements, while software and network applications are mandatory requirements. Category Subcategory Requirements Hardware CPU RAM Hard Disk Dual or more core processor and 2 GHz or higher. At least 2GB 5GB and more space, 7,200rpm or higher OS (*1) CentOS (kernel version 2.6.9) Software Web server (*2) Database (*2) Apache HTTP Server 2.0 series MySQL Community Server 4.1 or later Java (*2) JRE (Java Runtime Environment) 5-6 (*3) MassBank (*2) MassBank Linux version or higher *1 It should be installed. *2 These are installed in this manual. *3 The above recommended OS does not accept higher versions of JRE. 1.3 Flow Chart of Setup of Data Server and Manual Chapters 2. Setup of Linux OS - Installation and configuration of CentOS - Installation of Java 3. Setup of MassBank System - Installation and configuration of MassBank system 4. Check of Data Server - Checking operation of data server - Check operation of data server from the internet 5. Registration as a MassBank data server - Registration as MassBank data server - User ID and password - Prefix of Accession record ID Part 2-4

5 2. Setup of Linux OS Setup Linux OS by installing CentOS (kernel version 2.6.9) which is a freeware completely compatible with Red Hat Enterprise Linux. 2.1 Installation of CentOS Download Download CentOS (kernel version 2.6.9) from and save it to a CD, DVD, or other media Installation Run the installation from the OS installation CD, DVD, or other media. During installation, configure the OS for MassBank in the windows shown below. Note: These are not screen captures of every window in the installation process. Select Default when not specified. Before you start the installation, change the boot sequence so that the CD-ROM drive is first in your boot order. Press Enter key. Select Skip. Part 2-5

6 Select English. English is mandatory. Select a language for key board. Part 2-6

7 Select Custom. Part 2-7

8 When warning applet is appeared, select Yes. Part 2-8

9 Network for server should be manually setup later. However, select automatically via DHCP temporally. Select Enable firewall. Select Remote Login (SSH). Select Web Server (HTTP, HTTPS). Set Enable SELinux to Disabled. Select a language Part 2-9

10 Input the password of root account. Select X Window System. Click Details. Part 2-10

11 Select xorg-x11-xvfb. Select Web Server. Select MySQL Database. Click Details. Select mysql-server. Part 2-11

12 After reboot, setup process automatically begins. Part 2-12

13 2.1.3 Setup Window PC is rebooted after the installation of CentOS, then Setup window appears. Part 2-13

14 Configure the display setting Input user ID and password. Part 2-14

15 Press Next button, then CentOS starts. Input user ID and password. Part 2-15

16 2.2 Initialization of CentOS Confirmation of Needed Packages Confirm that packages including Apache and MySQL are installed. When they are not installed, install them. (1) Addition and deletion of application programs From the GNOME Panel menu, select Applications, System Settings, then Add/Remove Applications. Root password is requested. (2) Add necessary packages Click Details of X Window System. Part 2-16

17 Select xorg-x11-xvfb. Select Web Server. Select MySQL Database. Click Details. Select mysql-server. Part 2-17

18 2.2.2 Installation of Java JRE (Java Runtime Environment) 6 is downloadable from the page ( Java Help site ( is helpful for the installation of Java 6 on Linux. (1) Download Select Accept License Agreement button. For Linux x86 (32-bit), download jre-6u32-linux-i586-rpm.bin and save it on the desktop. (2) Installation $ su l Password: [Input 1] # chmod a+x./jre-6u32-linux-i586-rpm.bin # sh./jre-6u32-linux-i586-rpm.bin Unpacking Checksumming : Done. # - Input 1: root password Part 2-18

19 2.2.3 Configuration of Local Security Configure the firewall and SELinux. After making these settings, you must reboot the computer. From the GNOME Panel menu, select Applications, System Settings, then Security Level. Select Firewall Options. Select WWW (HTTP). Select SSH. Select SELinux. Clear the Enabled checkbox. When you modify the default setting, reboot the computer to reflect your SELinux settings Part 2-19

20 2.3 Confirmation of Settings Reboot PC to confirm the settings by displaying the desk-top window. Wait until the next window appears. Input user ID and password. Part 2-20

21 3. Setup of MassBank System Install the Linux version of MassBank Installation of the Linux version of MassBank Root password is requested on the installation of MySQL Download Download the Linux version of MassBank from Next, use your FTP software, terminal emulator, and then place the downloaded archive file into an appropriate Linux directory. Example : /home/massbank/massbank-1.8.1_lin.tgz Expanding Archive File Expand the archive file. $ su l Password: [Input 1] # tar xfz massbank-1.8.1_lin.tgz # cd massbank-1.8.1_lin # ls install.sh modules uninstall.sh - Input 1: root password Configuration of Tomcat Environment In the expanded directory, open the file "modules/startupscript/tomcat" using vi or other editor, and edit the following lines in accordance with your environment. export JAVA_HOME=/usr/java/jre1.6.0_32 [Setting 1] export CATALINA_HOME=/usr/local/tomcat [Setting 2] - Setting 1: JAVA_HOME: Specify the directory in which the JDK is installed. - Setting 2: CATALINA_HOME: Specify the directory in which Tomcat is installed. Note: Only change this value if you want to change the installation location. Part 2-21

22 3.1.4 Configuration of Installation Environment In the expanded directory, open the file "install.sh" using vi or other editor, and edit the following lines in accordance with your environment. # Apache Path APACHE_HTDOCS_PATH=/var/www/html [Setting 1] APACHE_ERROR_PATH=/var/www/error [Setting 2] APACHE_CONF_PATH=/etc/httpd/conf [Setting 3] APACHE_MODULE_PATH=/usr/lib/httpd/modules [Setting 4] # Tomcat Path DEST_TOMCAT_PATH=/usr/local [Setting 5] Setting 1: APACHE_HTDOCS_PATH: Specify the Apache document root directory. Setting 2: APACHE_ERROR_PATH: Setting 3: APACHE_CONF_PATH: Specify the Apache error directory. Specify the Apache conf directory. Setting 4: APACHE_MODULE_PATH: Specify the Apache modules directory. Setting 5: DEST_TOMCAT_PATH: Specify the directory in which Tomcat is installed. Note: Only change this value if you want to change the installation location. Part 2-22

23 3.1.5 Installation Run the "install.sh" file located in the expanded directory. $ su l Password: [Input 1] # sh./install.sh ********************************************* * MassBank System Installer * * version * ********************************************* Installation of MassBank modules. Are you sure(yes/no)? yes [Input 2] Starting install... >> service stop Sttopping httpd : [ FAILED ] >> file copy cp: overwrite `/etc/httpd/conf/httpd.conf'? yes [Input 3] >> change file mode >> service start Starting the xvfb service Starting MySQL : [ OK ] Starting the tomcat service Using CATALINA_BASE: /usr/local/tomcat Using CATALINA_HOME: /usr/local/tomcat Using CATALINA_TMPDIR: /usr/local/tomcat/temp Using JRE_HOME: /usr/java/jre1.6.0_32 Using CLASSPATH: /usr/local/tomcat/bin/bootstrap.jar Starting httpd : [ OK ] >> create database (root authority) Enter password: [Input 4] >> chkconfig xvfb on >> chkconfig mysqld on >> chkconfig httpd on >> chkconfig tomcat on Done. Please edit FrontServer URL of /var/www/html/massbank/massbank.conf appropriately. [Confirmation 1] # - Input 1: root password - Input 2: Whether to allow the installer to run (yes/no) - Input 3: Whether to allow files to be overwritten (yes/no) Note: If you see more than one request to authorize file overwrites, check them carefully before allowing. - Input 4: Enter the root password for MySQL Part 2-23

24 - Confirmation 1: Note down the absolute path of massbank.conf (the MassBank configuration file) 3.2 Initialization of MassBank Initialization needs the server host name setting in DNS. You must obtain the host name from your network administrator before the initialization Editing of MassBank Configuration File When the MassBank system was installed, the "massbank.conf" file was created (the default location is "/var/www/html/massbank/massbank.conf"). Edit this file using vi or other editor as follows, in accordance with your environment. <MassBank> <MyServer> <Name>Example MassBank</Name> [Setting 1] <LongName>Example MassBank</LongName> [Setting 2] <FrontServer URL=[ host name/massbank/] /> [Setting 3] <MiddleServer URL=[ /> <DB>MassBank</DB> <BrowseMode>3,5</BrowseMode> </MyServer> : : : - Setting 1: Name: The name of the site (short version) to publish data - Setting 2: LongName: The name of the site (complete version) to publish data - Setting 3: FrontServer URL: The URL to publish data Note: This is overwritten by the server hostname set in DNS Editing of hosts file Depending on the server environment, hosts file (/etc/hosts) should be edited. Confirm to network administrator. Part 2-24

25 3.2.3 Change of Preset User ID and Password of Administration Tool MassBank system provides Administration Tool for data management on data servers. The same user ID and password for Administration Tool are preset by the installer. They should be changed by the following procedure before data servers open to the public. $ su l Password: ******** [Input 1] # mv /etc/httpd/conf/.htpasswd /etc/httpd/conf/backup.htpasswd # htpasswd c /etc/httpd/conf/.htpasswd username [Input 2] New password: ******** [Input 3] Re-type new password: ******** [Input 4] Adding password for user username # - Input 1: root password - Input 2: New user ID for Administration Tool - Input 3: New password for Administration Tool - Input 4: Confirmation of new password for Administration Tool When you change user ID and/or password, restart web browser. Access Administration Tool from top page and confirm new user ID and/or password. Be sure to change the preset user ID and password of Administration Tool. 3.3 Reboot of Data Server Reboot the data server. Part 2-25

26 4. Check of Data Server Setup of data server should be checked by accessing from web browser on other PCs; [1] Top page, [2] Spectrum Search, [3] Record Index, [4-5] Administration Tool, and [6] WEB-API WSDL pages should be accessible. 4.1 Check of MassBank System Confirm that the top page is displayed when your browser accesses to the URL configured in Editing of the MassBank Configuration File. Also confirm the links that show their pages. Example: [1] Top page [2] Spectrum Search page [3] Record Index page [4] Administration Tool login *) *) Input user ID and password (see Change of Preset,, ) [5] Administration Tool page [6] WEB-API WSDL page Part 2-26

27 5. Registration to MassBank Group When your server and MassBank system are ready for launch, request the registration as the MassBank data server from the MassBank Group via or telephone. Contact : massbank@iab.keio.ac.jp Request of Data Server Registration On the request, MassBank group takes the following process for the registering data server. - Check the operation of data server - Check the access data server from other networks - Check the access data server by using SSH 5.2 Request of Prefix of MassBank Record ID Each MassBank record has the record ID that begins with a prefix consisting of two or three alphabetical letters. Prefix should be unique to research organizations or groups. The currently used prefixes are listed in the statistical table on MassBank page ( Part 2-27

28 Contact Please contact the MassBank Group if you have any problems, questions, and suggestions